[BioRuby-cvs] bioruby/lib/bio/appl emboss.rb, 1.5, 1.6 psort.rb, 1.9, 1.10 pts1.rb, 1.3, 1.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory dev.open-bio.org:/tmp/cvs-serv5347/lib/bio/appl

Modified Files:
	emboss.rb psort.rb pts1.rb 
Log Message:
* Changes due to the refactoring of Bio::Command.


Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** emboss.rb	17 May 2006 14:24:33 -0000	1.5
--- emboss.rb	14 Jul 2006 14:28:44 -0000	1.6
***************
*** 21,26 ****
  module Bio
  
- autoload :Command, 'bio/command'
- 
  # = DESCRIPTION
  #
--- 21,24 ----
***************
*** 76,81 ****
  class EMBOSS
  
-   extend Bio::Command::Tools
-   
    # Combines the initialization and execution for the emboss +seqret+ command.
    #
--- 74,77 ----
***************
*** 158,167 ****
    def self.retrieve(cmd, arg)
      cmd = [ cmd, arg, '-auto', '-stdout' ]
!     str = ''
!     call_command_local(cmd) do |inn, out|
!       inn.close_write
!       str = out.read
!     end
!     return str
    end
  
--- 154,158 ----
    def self.retrieve(cmd, arg)
      cmd = [ cmd, arg, '-auto', '-stdout' ]
!     return Bio::Command.query_command(cmd)
    end
  

Index: pts1.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/pts1.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** pts1.rb	5 Jun 2006 02:55:51 -0000	1.3
--- pts1.rb	14 Jul 2006 14:28:44 -0000	1.4
***************
*** 152,156 ****
      @uri = URI.parse(["http:/", @host, @cgi_path].join('/'))
  
!     result, = Bio::Command::NetTools.post_form(@uri, @form_data)
      @output = Report.new(result.body)
      
--- 152,156 ----
      @uri = URI.parse(["http:/", @host, @cgi_path].join('/'))
  
!     result, = Bio::Command.post_form(@uri, @form_data)
      @output = Report.new(result.body)
      

Index: psort.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** psort.rb	30 Apr 2006 07:13:39 -0000	1.9
--- psort.rb	14 Jul 2006 14:28:44 -0000	1.10
***************
*** 113,117 ****
          begin
            result = nil
!           Bio::Command::NetTools.net_http_start(@uri.host) {|http|
              result, = http.post(@uri.path, data)
            }
--- 113,117 ----
          begin
            result = nil
!           Bio::Command.start_http(@uri.host) {|http|
              result, = http.post(@uri.path, data)
            }